VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Nov 01 2016 - 14:39:40 CDT

Oh yeah, check these things first. If you’re still stuck, let us know.

Thanks Chris!
JC

> On Nov 1, 2016, at 11:45 AM, Mayne, Christopher G <cmayne2_at_illinois.edu> wrote:
>
> Andrew,
>
> I’m going to need the PSF and geometry optimized PDB file in order to try to reproduce your error. However, I already have one suspicion: when you load in the Gaussian target data, the parser attempts to assign the atom name based on the file name. In older versions of ffTK (I’m pretty sure that I changed this), when scanning multiple angles for carbonyls, the parsed atom name is e.g., O15-120a rather than O15. Make sure that you double check the atom name assignment in the QM Target Data section.
>
> Regards,
> Christopher Mayne
>
>> On Oct 31, 2016, at 9:38 PM, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
>>
>> I will take a look soon. Please bug me personally if you don’t hear anything within a couple days.
>>
>> Best,
>> JC
>>
>>> On Oct 31, 2016, at 2:15 PM, Eisenhart, Andrew (eisenhaw) <eisenhaw_at_mail.uc.edu <mailto:eisenhaw_at_mail.uc.edu>> wrote:
>>>
>>> Hello,
>>>
>>> I am attempting to complete the charge optimization for a fragment of my molecule using VMD-fftk (1.9.2). I am receiving the following error code when running the optimization.
>>>
>>>
>>> measure bond: must specify exactly two atoms in a list
>>> measure bond: must specify exactly two atoms in a list
>>> while executing
>>> "measure bond "[$temp1 get index] [$temp2 get index]" frame $i"
>>> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 215)
>>> invoked from within
>>> "::ForceFieldToolKit::ChargeOpt::optimize"
>>> (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
>>> invoked from within
>>> "::ForceFieldToolKit::gui::coptRunOpt "
>>> invoked from within
>>> ".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
>>> invoked from within
>>> ".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} { .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed; .fftk_gui.hlf.nb.chargeopt.runOpt in..."
>>> (command bound to event)
>>>
>>> There are few similar questions on the mailing list already, but no solutions that have worked for me. I've tried simulated annealing and downhill with no success.
>>>
>>> I can replicate the error when loading as few as one log file.
>>>
>>> Here is a link to my box folder that contains my .log and other initial files. https://uc.box.com/s/3vye3uqw8d90vpqyn0qgm08k4s5sgf18 <https://urldefense.proofpoint.com/v2/url?u=https-3A__uc.box.com_s_3vye3uqw8d90vpqyn0qgm08k4s5sgf18&d=DQMF-g&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=F5kKc5Rhmmlee4S-dJMey3-z8c6aer0EfW-sSkEaAJ0&s=P1kBONdiuIUOjtm29TKzU2sVUpYAuHXL8fRv9R10oBI&e=>
>>> This folder contains the Gaussian input files i used to generate the log files. https://uc.box.com/s/udepalaygv1sq2xqwwka9ox10vl3mr5j <https://urldefense.proofpoint.com/v2/url?u=https-3A__uc.box.com_s_udepalaygv1sq2xqwwka9ox10vl3mr5j&d=DQMF-g&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=F5kKc5Rhmmlee4S-dJMey3-z8c6aer0EfW-sSkEaAJ0&s=oiUjKnxEn4NwtDxvAK7bv99ogAj2OJo8ZyzloLtRUpw&e=>
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__uc.box.com_s_ku0ujld45bjirmut8xbelcxlukuhoq42&d=DQMF-g&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=F5kKc5Rhmmlee4S-dJMey3-z8c6aer0EfW-sSkEaAJ0&s=es8HyFikXoG8quIaeQhLX5_TtM8U1Zoygt2rSHqzjco&e=> <https://urldefense.proofpoint.com/v2/url?u=https-3A__uc.box.com_s_3vye3uqw8d90vpqyn0qgm08k4s5sgf18&d=DQMF-g&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=F5kKc5Rhmmlee4S-dJMey3-z8c6aer0EfW-sSkEaAJ0&s=P1kBONdiuIUOjtm29TKzU2sVUpYAuHXL8fRv9R10oBI&e=>
>>> Thanks for your time!
>>>
>>>
>>> -Andrew Eisenhart
>>
>